Freedom is the Right of All Sentient Beings
by Gehenna79
Summary: Six years have passed since the Battle of Zion, and the Machines and Zion have struck an uneasy peace. But now, an alien force, made of sentient machines called the Decepticons, have invaded. Now, the Machines, Humans, and Autobots must make an alliance to stop Megatron's ultimate plan, but will they be able to trust each other?


**Chapter One : A New War**

* * *

Six years had passed since the Battle of Zion, and the peace treaty between Zion and the Machines had been formed midst mutual distrust on the part of both parties. However, things had been better than they had ever been, with more and more humans being allowed to leave the Matrix based on their personal choice alone.

So when Morpheus received a message that day, July 1st, 6 NEO*, that the Council wished to see him because of an emergency, Morpheus had no idea what that could be.

Quickly, he dressed and ran to the elevator, taking him down the many levels of Zion, deeper and deeper into the Earth's mantle. All around him were people lit up with purpose, running to and fro on their work. Zion was expanding, growing larger, and new resources had to be obtained and processed. Morpheus could hear the sound of beeping trailers backing up and the hammering of jackhammers on the walls. One of the problems that Morpheus was aware of before, was a growing shortage of food.

He finally reached the Council room about ten minutes later, and saw that it was half full, with the Council at their seats towards the back, wearing their usual assortment of colored robes, a style that was decidedly ancient and elegant in contrast to the dull grey of technology around them. Standing in front of them was another person, and when that person turned to Morpheus, Morpheus was shocked to stillness, his mouth agape.

It was Neo.

"Morpheus," Neo said with a pained smile, "Its good to see you."

"How...we...I thought you were dead."

"I was. But the machines brought me back."

Instinctively, like a reflex, these words immediately hit Morpheus in the gut, putting him on edge. He stiffened at the words and then said, with an awkward laugh, "Well. I suppose if you cheated death once, you could do it again."

"You could say that."

"Morpheus," interrupted Councilor Hamann, "I hate to bother this reunion, but unfortunately our business cannot wait."

"Apologies," Neo and Morpheus said at the same time, then looked at each other with slight grins.

"Neo's arrival by itself is shocking enough," continued the Councillor gravely, "But he has just told us some strange news."

"What kind of news?" asked Morpheus.

"According to Neo," said Councillor West, a bearded man with dark skin like Morpheus, "We face a new threat, from an unknown stimuli. The machines have reacted to it, but we're not sure what it is. Apparently its been important enough for them to recall all Sentinel forces back to the city...on defense."

"How do you know this, Neo?" asked Morpheus.

"During the battle with Agent Smith, my mind became controlled by him, in order to unbalance the Equation of the Matrix again. In reaction, the Architect, the creator of the Matrix, destroyed Agent Smith. However, my mind wasn't destroyed, it was floating around in the Matrix, separated from my body as if in...limbo, I guess you could say. It took three years, but the Machines created an interface that allowed my mind to be grasped and returned back to my body. But in the process, I have a connection to the Machine mainframe...so all of them."

"Then do you know what this threat is?"

"No, but only because _**they**_ do not know what it is, and I can receive no visual, just impression of feelings and information through code. All I know is that they are very large...and very powerful, and they are not from this world."

"Are you shitting me? We're talking about extraterrestrials now?"

"I wish I was crazy as well Morpheus...but I'm unfortunately not."

"It was a little hard for us to accept as well," said Councillor Dillard, a stern older woman with silver hair, "But Neo is responsible for all of us still standing here, so we owe him our trust and belief."

_But the machines re-built him, _thought Morpheus to himself. He could tell by some of the looks of the other Councillors, that some were thinking the same thing.

Concordantly, Councillor Bradley, a man with long hair and grey sideburns said, "My only problem is, how can we trust that this is indeed the real Neo? If he was re-built by the machines, then...he could be controlled by them? What if this is a machine?"

"Are you ridiculous?" replied Hamann, "The machines don't have that kind of replicator technology."

"As far as we know."

"Yes, but if they did, why would Neo tell us he was machine-built? It would be a major breach of logic on their part to not hide this fact, when it would make us more cautious."

"Maybe they want us to be divided, and this is all a trap."

Neo raised his hand, and they were silenced. He replied, in a calm even tone, "I understand your concerns, and I respect them. So in order to prove that I am not a tool of the Machines, I would like to request that Councillor Hamann and Morpheus accompany me to visit the Oracle while en route to our destination. She can vouch for me, and you will have two more convinced for you."

"The Oracle is a machine too as well," complained Bradley.

"Now I must say that is indeed absurd," interrupted Dillard, "The Oracle has been with us since the beginning, and led us to where we are now. I agree with this plan. Councillor Hamann?"

"Of course. It has been some time since I have been jacked in, but I'm sure I can manage," he gave a wry smile to Morpheus and Neo.

"Very well, the matter is settled. After visiting the Oracle, Morpheus, Neo, and the Councillor will go with Neo to investigate the location of the new Machine stimuli. All in favor?"

Most everybody put their hands in the air, save Bradley and two others. "Then we shall allow this. Godspeed, you three."

* * *

Twenty minutes later, they were en route to the _Victory, _a new hovercraft built from the many pieces of scrap metal left by the dead Sentinels during the battle of Zion. They were walking down a hallway, when suddenly, Morpheus, Neo, and Councillor Hamann were stopped by a firm, commanding voice. "Morpheus," he said, "Stop right there."

Commander Lock was a hard, impervious man with a dour face and dark skin with dark hair. He had a perpetual frown whenever in Morpheus' presence. Strangely though, Morpheus still respected him, for without him, the city would still not have held as long as it did. He just needed a little more faith, was Morpheus' opinion.

"Sir," said Morpheus, as did Neo.

Lock looked like he had been just slapped across the face. He stammered, "Y-y-you. What the hell are you doing here, Neo?"

"I have returned."

"I see that, smart ass. You want to elaborate?"

"We don't have time."

"Yes," interrupted the Councillor, "We must depart quickly, in order to jack into the Matrix."

"Why wasn't I told about this?"

"The Council was planning on telling you as soon as they saw fit. Neo has returned with news, that you should hear. Tell him, Neo."

Neo looked a bit awkward, but he cleared his throat and said, "Due to some complicated circumstances, I have a connection to the Machines...err...all of them, and that has allowed me to know that they are facing a new threat...from outer space."

Morpheus chuckled.

"Goddamn it Neo, you expect me to believe that shit!"

"I don't care what Neo expects," said the Councillor sternly, "That even in strange circumstances such as these, to obey the will of the Council. Besides, I am going to go with them to ascertain the truth before we take any action."

"Whose ship are you taking?"

"My own," said Morpheus.

"You didn't ask permission for a departure."

The Councillor coughed, "Departure request granted."

Lock began to fume, then finally said, "Alright, I guess I will take my leave then Councillor, and await a sitrep at your arrival."  
He did the most curt, forced bow ever, and then ran off.

"I almost feel bad for him," said Morpheus.

"Yeah, I did, but we should get going," agreed Neo.

"Alright. But I have a few questions along the way."

"I'll try my best to explain."

"If you're still here, then does that mean Agent Smith is still out there as well?"

"Its possible," said Neo gravely, "As of yet, I have not run into him, but that may be because he has not been reassembled...at least not in code. Or maybe the Source destroyed him. I do not know. Other than the testing of my body, the Machines talked little to me, and I didn't feel too chatty."

"Why did the Machines rebuild you though? What purpose did they have in that?"

"I don't know that answer. May want to ask the Oracle if you get the chance."

"Do you think that they respected Neo for defeating Agent Smith?" suggested the Councillor, "Or do they not have that concept?"

"They are capable of feeling anything we feel," explained Neo as they stepped over some loose pipes.

"How do you know that?"

"Maybe you will meet Sati, and she can explain."

"Who?"

"A program. Born from two other ones. I met them before my uh...death."

The Councillor shook his head as they walked into the hangar, "Never mind."

"One last thing Neo," said Morpheus as they began to board, walking along a long ramp, "Where's Trinity?"

Neo stopped and paused, silent and staring at the floor for a moment. Then he looked back and frowned, "She's dead, Morpheus."

Morpheus felt as if he had been stabbed. He put a hand on his pal's shoulder and said, "I'm sorry, Neo."

"Not as sorry as I am, Morpheus."

* * *

It was raining as they entered the Matrix through a deserted alleyway. The place was strewn about with refuse, open trash bags that assaulted their minds with a haze of odiferous bile. A cat program arched its back and hissed at them, then ran off. It was cold out, and there were cars driving on the road head, their lights blurring as they flashed by.

"Its been six years," said Neo, "But seems nothing has changed."

"Only one percent of the Matrix's inhabitants can refuse the program. The others were never ready. The shock would be too much, they wouldn't want to live in the real world."

"A sad truth," agreed the Councillor. While Neo and Morpheus were wearing their usual dark attire, the Councillor was wearing a grey business suit with a purple tie, and an onyx cane with a sapphire on the top.

"And we have no way to stop the Machines from using the inhabitants as batteries. We just have to accept things for the way they are."

"Don't worry," assured the Councillor, "You've done enough. Civilization will rebuild and one day, all of mankind will be free."

"I hope you're right. And I hope that the Machines didn't just hear that."

The Councillor laughed, "Sorry my boy."

They hailed a cab and took it down to the center of the city, the name of which, Morpheus did not know, but it wasn't American or European. There were a lot of asian blue-pills all around, running about in the rain on business, trying their best to stay dry, not understanding that they had never been dry in their lives.

Finally, they stopped by the entrance to a tall apartment building. They all got out and entered inside, instantly receiving relief from the rain. They entered a long hallway with bland cream-colored walls and red carpet.

"Down this hall?" asked Hamann.

"Yeah," said Neo, "I think."

They walked down the hall, until they came to a single doorway. Neo opened it and they went in one at a time. Waiting inside a room with wooden floorboards and walls, was Seraph, meditating on the floor. Without looking up or opening his eyes, the program-warrior said calmly, "She has been expecting you."

"No surprise there," said Morpheus.

"You may go in. I know you are all real. It has been some time, Mr. Hamann."

Hamann bowed.

They went into the apartment of an old woman. The smell of baked goods and candles was saturated without; the walls were lime green, there were throw-rugs on the floor and covers on the sofa cushions, quaint pictures of people in old-fashioned photographs in wooden frames. Everything seemed matronly, just like home, or what anybody in the Matrix wanted their home to seem like.

The Oracle was in the kitchen, hand-kneading some cookies with the help of Sati, who had now grown to resemble a young teenage girl. Neo reflected on the fact that she had had to chose that, since Programs didn't age as humans did.

"Come in boys, they'll be freshly baked in about twenty minutes. Take a seat, and I'll be right with you."

The three of them took a seat, and the Oracle came down next to them. She lit a cigarette and took a draw and said, "Neo, you're looking well I see."

"Thank you. I feel well. For the most part."

"I think I know what you mean. Morpheus?"

"I felt a little purposeless at first but..."

"You got over it when you realized that the work was just getting started?"

He smiled, "Yes, ma'am."

"And Hamann, its been some time. You never thought you'd live to see the day the Machines let your people live free?"

"No, I didn't."

"But you're still troubled."

"A little, yes."

"That the Machines still hold the power, and Zion is still at their mercy, should they decide to break the treaty?"

The Councillor nodded, "Yes."

"Well good news for you, because you're about to get a chance to even the playing field, so to speak."

"You knew this anomaly would happen?" asked Neo.

"I knew that something of this nature would happen, but sadly, to my own disappointment, I didn't get it right as to when, because you can't really predict when an alien race will arrive on your front door."

"So its true," said Morpheus.

"Of course. Would you ever doubt Neo?"

"No," he gave Neo a look, "I just couldn't believe it myself."

"Its okay Morpheus," said Neo, "I don't hold it against you."

"Well that's good," the Oracle laughed and took another drag, "But you got some problems ahead of you, and each one of you is going to get different advice today. But first, let's cover the basics. Sati, could you go in the other room please?"

"Yes, Oracle"

"Thank you honey," the program left, "Now. These extraterrestrials have the machines scared. Not of what they are, but of what they aren't."

"Okay," said Morpheus.

"They always assumed that if this did happen, it would be on their terms. A space program was always in the works in the Machine city, but it hadn't ever taken off yet, because they needed a reliable power source other than human batteries. It would be way too impractical. They always figured that the aliens they would run into as well would be machines as well, their sort of arrogance believing that machines would be the only ones capable of getting that far. But...they were only half right.

"The aliens they have encountered are machines, but they are not like us. They aren't run by code. Some might say that there's something...unnatural about them. I don't know it for sure, but these aliens killed a large number of the Sentinels, and they fear that this is just the start of an invasion. They want to protect themselves and build up their defenses."

"Who are these aliens? Could they or would they help us?"

"That I cannot tell you for sure," the Oracle shrugged, "It could be possible, but remember that destroying the Machines, means destroying billions of human lives plugged into the Matrix as well. There's no guarantee that these new machines will care. They might be a danger to both of you."

"But if the machines can't stop them," asked the Councillor softly, "Who can?"

The Oracle frowned and replied, "Nobody."

* * *

Footnote 1: NEO stands for New Era of Order, Zion's new system of dating.

I do not own the Matrix or Transformers.


End file.
